ME3: Project Gemini
by LapisDragon
Summary: This time the Illusive Man has gone too far. While scanning planets for resources, Shepard encounters a group of outcast colonists and makes a discovery that will shake him to his very core and forever change the way he looks at Cerberus. Not an alt-end
1. Chapter 1: Creche

Project Gemini: Chapter 1 – "Creche"

This five-chapter story takes place during the events of Mass Effect 3, roughly between the events of Priority: Palaven and Priority: Sur'kesh. The only plot assumptions made are that:  
- Commander Shepard is male with blue eyes (though feel free to mentally replace all occurrences of the word 'blue' with the color of your choice),  
- Ashley Williams survived Virmire and was hospitalized after the events on Mars, and  
- Shepard and Garrus survived the suicide mission against the Collector's base.

All other divergent plot decisions I leave up to you, the reader. Enjoy.

* * *

"No Reaper signatures detected, Commander." Joker's voice echoed across the CIC, causing tensed muscles to visibly relax among the crew members. Commander John Shepard continued to stand at attention before the galaxy map, his pale blue eyes moving as they scanned the information from the various ship sensors flowing across the holo-display.

"Come about and make for the third orbital ring, Joker. We'll start scanning when we reach the planet there. And keep an eye on our escape vector. We don't need another surprise like last time." The Normandy had barely escaped a Reaper ambush in the last sector. Seeking a quick escape from the system, Joker had reversed their heading, right into the grasp of another Reaper which had followed them out of FTL. Only Joker's expert flying and lightning fast reflexes had gotten them through the Mass Relay in time.

Several random FTL jumps later, the Normandy found itself in this unnamed system. Five planetoids orbited a main sequence yellow star, the third of which appeared habitable according to EDI. A scanning pulse would be risky, with the ever increasing Reaper presence throughout the galaxy, but the Normandy was critically low on resources and the credits from any salvage found would go a long way towards continuing the fight against the Reapers and Cerberus.

Here we go, Shepard thought, activating the scanner pulse. A sonar ping sounded, for the benefit of the operator rather then serving any functional purpose, as the pulse wave spread through local space. Immediately a red circle appeared on the representation of the third planet. "Sensors have detected an anomaly, Shepard" EDI announced.

"What are we looking at? Derelict ship, lost artifacts, or more wayward marines?" Shepard demanded, bringing up the scanner results on the holo-display. An image of the world appeared, covered in blue liquid with green and brown land masses scattered sporadically across it. Text along side the image indicated the liquid was mostly water, with a breathable atmosphere and signs of advanced plant life being prevalent. A blinking white dot indicated the location of the anomaly.

"Anomaly identified. There appears to be a small settlement on the primary landmass. Sensors show signs of habitation modules and cultivated land. No signs of defensive systems or air/space vehicles."

"Give me a close up of the habitation area, let's see what we're dealing with here" Shepard ordered. The image of the planet on his datapad changed to one of an aerial view of a small settlement. Shepard counted twelve standard habitation modules, designed for multiple families, and several larger communal buildings. Some of the buildings were connected, others were independent, but all of them circled a central platform. Alliance standard colonial housing, but what are they doing out here?

"Commander, zoom in on the building at two o'clock. There's a logo on the wall" Traynor chimed in from her station beside the holo-display. Shepard touched the building on the screen, zooming in and waiting for the image processors to resolve the picture. As the artifacts cleared, Shepard felt his heart drop. The logo was unmistakable. Cerberus.

* * *

"What's a Cerberus base doing way out here?" James asked, leaning against the old conference room table.

"Whatever they've found here, the Illusive Man wants it, which means it's something we don't want him to have." Garrus responded, flicking through images of the settlement on his datapad, trying to identify possible threats.

"We're going to have to send a ground team. We'll infiltrate, assess, and either repossess or destroy as appropriate. Liara, you and James are with me. Garrus, stay on the ship, see if you and EDI can re-establish contact with Admiral Hackett. I don't like how isolated we are out here. Ash, you're..." Shepard stopped, realizing once again that Ashley Williams still lay in a hospital bed on the Citadel. The rest of the crew pretended to take no notice of the mistake.

"Anyway, we'll take the shuttle down and come in low behind this ridge. From there, we'll make our way in on foot. Full loadouts people, we don't know what we're going to find here."

"Yes, Sir!" James said, snapping to attention with unrepressed vigor. He was anxious to get back into the fight after having to sit out the last couple of away missions. The rest of the crew filed out of the room more quietly to begin preparations.

The door to Shepard's cabin chimed, awaiting his approval before allowing entry to whoever waited outside. Giving approval, Shepard finished snapping his black N7 gauntlets into place before looking up to see Liara standing in the doorway, a concerned look on her pale blue face.

"I'm worried, Shepard. Something doesn't seem right about this place."

"I know; I feel it to. Why doesn't the computer have any information about it? Even EDI isn't finding anything in her Cerberus records. What was the Illusive Man trying to hide out here so badly that we don't even have a name for the planet?"

"It's more then that. In the images of that place the people look so peaceful, almost idyllic. Aren't they concerned about the Reapers?" Liara paused for a moment, biting her lower lip. "And I'm concerned about you. You're still dealing with Ashley's injury. On Palaven you put it aside to help the Turians, but I can see that it still bothers you how easily she was hurt."

Pulling the small Asari into a hug, Shepard gave her a squeeze. "It's alright; it was just a slip of the tongue. I got an email from her just before we lost communications, she said she's beginning rehab and is anxious to get out of that bed. She'll be ready to rejoin us before you know it. It'll be just like old times."

"You mean running around the galaxy chasing Saren while dodging Geth at every turn" Liara responded with a quirk of humor on her lips.

"Yep, only this time it's Reapers instead of Geth. Makes it a bit more challenging, but hey, at least it's not dull, right?"

"Only you could say that with a straight face and mean it, Shepard." Liara said with a smile. Reluctantly leaving his embrace, Liara turned towards the door, pausing at the threshold and turning back. "Just use that charm on whatever we find down there and they'll be happy to quit Cerberus and join us."

"Well, if they don't, there's always Plan Triple-B."

"Triple-B?"

"Yep, Bombs, Bullets and Biotics"

* * *

Watching the shuttle lift off from the landing zone Shepard scanned the terrain, weapon ready, while Liara analyzed the air. Finally she looked up from her Omnitool. "No signs of contaminants in the air. Readings say it's safe to breathe." Shepard and James removed their helmets, disengaging and stowing away the breathing apparatus before putting them back on again. Liara simply removed her breathing mask and put it in her pack. The temperature was pleasant; slightly cool with a bit of a northern breeze blowing from the direction of the settlement. Motioning James to take the lead, Shepard fell in behind him, watching the sides while Liara covered their rear.

Eventually the trio arrived at the outskirts of the settlement. Pulling a spare rifle scope from his gear, Shepard scanned the buildings, once more feeling a slight shudder upon seeing the Cerberus logo so prominently displayed. People moved throughout the settlement, men in rough-edged colonial garb talking under the shade of an awning, others hoisting tools of various sorts as they walked along the central path. Something was strange about the men, but Shepard couldn't quite say what. Continuing his inspection, Shepard found several women hanging laundry around what must be a communal wash area, while other scrubbed clothes in large buckets. Shepard even saw children playing in the grass, rolling and tumbling in the green field.

What Shepard didn't see was a single weapon, not even a pistol. Even the poorest alliance colonial knew to keep a weapon handy at all times. Shepard's youth had been spent on Mindoir, a small colony that had managed to eke its way to sustainability on a far less forgiving world then this one. On Mindoir everyone had carried a weapon, though this hadn't helped when the slavers had come. What made these colonists feel so safe that they would fore go even that much protection?

Pulling back from his observation point, Shepard compared notes with James and Liara, who had also observed the settlement with binoculars and scopes from other angles. "I don't see any signs of Cerberus troops or material, other then the buildings. How about you"

"No guns, no shield generators, no barricades. It's like these people don't care if they're wiped off the map without a fight." James said, frowning.

"Something puzzles me." Liara said, working with her omnitool. "I counted thirty-two individuals: four male, twenty female, eight children. All the residents I saw appear to be around the same age. I didn't see anyone older then their late twenties and, other then the children, no one younger then their early twenties. None of the children appeared older then five. Even for a young colony, there ought to be a greater diversity in ages then that. And, especially the men, they all appear the same. The women at least vary in height and weight and build, but the men I saw all appear to be within 6 inches of each other, with same basic builds and body structures."

Looking up into Shepard's eyes, Liara looked even more troubled then back in the cabin on the Normandy. "Something doesn't feel right about this, Shepard."

"That's what we're here to find out, Liara. We'll wait for evening, see if anything else happens, then move in. For now, let's report back to the Normandy. Maybe they've found something we missed."

* * *

As the sun began to set, a group of settlers arrived, tiredly carrying tools and pulling carts loaded with produce of some sort. The men were greeted by the women with hugs and kisses, the children running out to climb on the carts. Nothing appeared out of ordinary until Liara spoke. "Sixteen men, Shepard. That brings the total population to forty-eight: twenty men, twenty women, eight children. Look at the population split. No singles; everyone has a partner of the opposite gender."

"Loco, I'm not sure about this. Maybe we glass the place from orbit and head back to the real fight, eh?" James asked, nervously.

"No, I want to know what's going on here. It's time we went in and started asking questions. Keep your weapons holstered, we're not looking to start a fight."

"Yet." James muttered, holstering his shotgun.

Shepard picked his way out of the grove of trees in which they had observed the settlement, making his way steadily towards the lights. As the party approached, people turned and whispered, pointing at them, particularly at Shepard. Women with children clutched them tightly, while others glared. The men, oddly, simply stood relaxed and smiling, though smiles turned to astonishment as Liara entered the light. Finally the group reached the central platform, upon which several of the males had gathered.

Approaching the platform, Shepard opened his mouth to speak, but was interrupted as one of the men stepped forward, raising his arms.

"Brother! Welcome home! It is always good to meet another member of the family."

Shepard looked up into the man's face as Liara gasped and James grunted in disbelief. Blue eyes met blue eyes as Shepard looked into the man's face and found his own.


	2. Chapter 2: Castor

Chapter 2 – "Castor"

This story started out as an example of a 'misapplied trope'. Playing through Mass Effect 3 for the first time as a male Shepard, I quickly reached the point where The Illusive Man is sitting in front of his display as a mysterious man walks towards him and stands behind his chair. Obviously this was TIM's new right-hand, now that Miranda had defected. My first thought was (and I literally said this out loud), 'Oh crap, they cloned Shepard!' As players we later learn who this mysterious man is, but that first impression stuck with me throughout the rest of the game.

When I mentioned this mistake to my good friend (who is a certifiable Mass Effect fanatic), she laughed and said how awesome it would have been if that were true (along with questions regarding my mental state). When I explained the reasoning behind that assumption, she agreed that it was something TIM would have done. Subsequent conversations expanded on the idea, forming a basis of how it could happen and the implications. Throughout these conversations she insisted that I had to write it out. Well, this story is the result (note, she helped with the plot seed and some of the details. But even she doesn't know how this ends insert maniacal laugh here).

* * *

"Brother! Welcome home! It is always good to meet another member of the family."

Shepard stood in stunned silence as around them the men began cheering and clapping. Liara had been mostly right. All the males were the same age, height, and build but, more importantly, they were all… Shepard.

There were small differences, of course: a scar here, a darker complexion there, different hairstyles and facial hair, but on a fundamental level they were all him. _What is going ON here?_ Time seemed to slow to a crawl as the enormity of what he was witnessing crashed down on him. _They're all… me._ Two of the men on the platform reached down and pulled Shepard up with them, clapping him on the back and inspecting his armor.

"Strange clothes you wear, brother. What are those meant for, rolling down hills?" The crowd of men laughed heartily. "And is this your wife? That's an odd hairstyle, but to each their own, right?" One of the men nudged Shepard in the ribs. "Well, regardless, I'm sure the womenfolk will want to talk to her straight away. Come, tell us your name so we can greet you properly!"

Shepard was silent for a long moment, still grappling with the shock. James looked like a caged animal, head turning this way and that while his hand seemed a twitch away from drawing his shotgun, despite being utterly ignored by the crowd. Liara just stood still, as stunned as Shepard. Finally, Shepard shook off the friendly encouragements of those around him and stepped forward. "My name is John Shepard, Co…" Before he could finish, the crowd roared "WELCOME, BROTHER JOHN!"

"Excellent, now that you've been welcomed we'll find some lodging for you and your lovely wife, and your escort can return to the stars. Tomorrow we'll add you to the work rotation and show you around our community."

"Wait, my escort?" Shepard asked, puzzled.

"Certainly! Your friend here can't stay", the man said, pointing towards James. "He's not part of the family. Don't worry; it was the same for all of us. It will be hard to say goodbye, but we all went through it and you'll quickly find friends among your new brothers and their families."

"Commander, what's going on here?" James asked with a note of panic in his voice.

An idea popping into his head, Shepard hopped down from the platform and pulled James close as if into a farewell hug. "For now, let's go along with them." Shepard whispered into James' ear. "I want to get to the bottom of this. Head back to the Normandy and have EDI focus her scanners on the village and the fields around it. Something else is going on here and I want to know what."

"You sure, Commander? There's a lot of them, I mean, you… gah, you know what I mean!"

"Go, James. We'll stay in contact and if it looks like trouble, we'll call for help. Till then, stay on the ship and keep an eye on us."

After a moment, James stepped back, saluting and saying "Yes, sir" before turning and making his way back towards the landing zone. Shepard turned back towards the crowd.

"SHEPARD!"

Shepard heard Liara's shout and noticed a swarm of women taking her by the arms and pulling her towards one of the buildings.

"Wait!" Shepard called and tried to rush after them, but was restrained by several of the men.

"That's women business, Brother John. We don't get involved in that. Don't worry; your wife will be fine. I'm sure they just want to throw her a welcoming party. Come, you've got your own party to attend!" What that, Shepard was pulled towards a communal building; a pre-fabricated structure nearly opposite from the one Liara was being drug to. Shepard watched helplessly as they were pulled apart, Liara's pleading eyes meeting his until the door closed between them.

* * *

Shepard spent the evening fruitlessly trying to gain information from the men. They were more than willing to talk of course, in between drinks of some sort of sweet nectar. The problem was they didn't _know_ anything; terms like Cerberus, The Illusive Man, and the Alliance brought nothing but blank stares or attempts at humor. 'Reaper' was apparently the name of one of their agricultural implements. Even mention of other races like the Turians and Asari causing nothing more then odd looks and calls for more drink.

All Shepard could gather was that the village had always been here, and that each of the men had been brought here individually with their wife and an escort who had left immediately afterward. No one knew where the escorts went after leaving except that they 'returned to the stars'.

Without an orbiting moon, and in an equatorial climate without obvious seasonal changes, time keeping was sporadic and unreliable at best. The calendar was primarily based on crop rotation, with four cycles called Plant, Tend, Harvest and Fallow, each of which lasted as long as the women said it did. The working day lasted from sun-up to sun-down, with no indication as to how long that took in standard galactic time-keeping terms.

What Shepard did learn in abundance were the rules of the settlement. Men were expected to work in the fields during the day, with periodic breaks for water and food, except when summoned for a task by the women. The women handled all affairs in the village, including cooking, cleaning, and repairs and maintenance. During the Tend and Fallow cycles, at a time determined by the women, each man would be called into the clinic for a health assessment. Otherwise, interactions with the women were forbidden except at night with his wife, and only with her consent.

Shepard began to feel his attention drift and his vision begin to blur. _Am I that tired, or is this drink some kind of intoxicant?_ Alarmed, Shepard tried to rise to his feet, but stumbled and fell. The men laughed and some of them helped him up. "It's always like that at first, Brother John. You'll be used to the festival drinks by the time our next brother comes. Here, we'll help you to your bed. I'm sure your wife is there waiting anxiously for you." Barely able to shake his head in denial, Shepard was lifted by two of the men and carried out of the building and into another, with a darkened main room and separate bedroom. The bedroom had a large, two-person bed and a pair of dressers, but little else. The men helped Shepard, barely conscious, out of his armor and into the bed before quietly closing the door and returning to the party.

Struggling for consciousness, Shepard dimly heard the soft grind of gears as his bed slowly lowered into the floor.

* * *

"Careful, he's waking up. Check his restraints, quickly!"

Shepard groggily awoke to the sound of feminine voices around him. Attempting to sit up revealed that he had been secured to some form of canted examination table with his head slightly higher then his feet. A quick assessment also revealed that he had been bound with straps around his ankles, wrists, thighs and chest. He was not wearing his armor nor, he noted with a touch of embarrassment, anything more then a pair of boxers.

Looking around, Shepard found himself in a modern medical lab. A variety of instruments around him glowed with bright displays and blinking lights. _Ah, now we're getting somewhere. But where is this?_ His eyes finally focused on a group of women studying him from behind a bank of computers and a protective glass wall. He recognized several from the gathering the previous night, but what struck him now were the lab coats the women wore, specifically the Cerberus logos on their sleeves.

"Where am I? What am I doing here?" Shepard groggily demanded.

"We were hoping you could tell us that, Commander Shepard." One of the women, slightly older then the others with brown hair tightly pulled back into a bun, stood up from the console. "Did the Illusive Man send you here? My understanding was that Project Lazarus and Project Gemini were to have no interaction with each other. Has that changed?"

"Project Gemini?"

"You don't know, then?

"Know what, that you've been making copies of me? Cloning me and storing those clones here on this backwater planet for who knows how long?" Shepard futilely struggled with his restraints. "What have you done with Liara?"

"Your pet Asari is safe, for now. Whether she remains that way depends on your answers. Now, how did you find this place?"

"Dumb luck. Now let me see her!"

A shock ran through him as electrodes on his temples fired. Shepard gritted his teeth to prevent a scream from escaping. "Not just yet, Commander. We're not done here. Your presence may yet prove useful, but for now you're a spanner in the works and I need to determine the best way to extricate you without damaging things further."

The woman, who Shepard decided to call 'Hairbun', waited for Shepard to stop shaking from the electricity before continuing. "Now, you claim you found us by 'dumb luck', but what are you doing in this sector anyway? There are no Collectors here for you to fight, Commander, no Prothean ruins to explore; just this inconsequential pile of rock that just happens to be in the right place and composed of the right things to support human life."

Shepard shivered as the tingle from the electricity finally subsided. "We were running from the Reapers, looking for resources, allies, anything to slow the Reapers down until the Crucible can be built."

The women at the console gasped, turning to each other, their voices overlapping. "The Reapers are here? Already? No, that can't be!" Hairbun slapped the top of the console, shocking the scientists into quiescence, before turning back to Shepard. "The Illusive Man assured me personally that we would have time to complete Project Gemini. What happened?"

Hairbun's voice rose as her agitation increased. "We received new clones every month on schedule, in accordance with the plan. Then nine months pass without a single word; no communications, no new clones, nothing! Now you, the progenitor, show up out of nowhere and declare that the Reapers have invaded and that you, our best hope and the sole reason behind both Projects Lazarus and Gemini, _can't do a thing about it_?"

"Maybe we can help each other, Doctor…?" Shepard asked.

"My name is Doctor Samantha Martin, Commander. I am the lead researcher here and the commanding officer over Project Gemini. As you've no doubt surmised, these panicked hens are my research assistants, as are all of the members of this research installation. And yes, before you ask, we are all female to prevent confusion among the men. The last thing we need is for them to start asking why 'that guy' doesn't look like the rest of them, after all."

"The men, the… clones; they're all clones of me, aren't they? How long have you been doing this?"

"Your genome was compiled from your corpse at the beginning of Project Lazarus. Project Gemini began as a fallback option should Project Lazarus fail, as seemed increasingly likely in the early days of the project, before Commander Lawson was assigned to the project."

"If you can't resurrect me, clone me? Either way, the Illusive Man gets his Commander Shepard, right?"

"That was the plan at first. Then Project Lazarus began to make strides and its projected chances of success rose. Project Gemini was nearly scrapped until I approached the Illusive Man with an idea. Why have just one Shepard running around when we could field an army of you, each with all your skills and Lazarus-enhanced abilities"

Shepard winced, once again appalled at the depths the Illusive Man, and Cerberus, would sink to in order to further their goals.

"That was the plan, and the Illusive Man agreed to it. Project Gemini was officially cancelled and was wiped from all Cerberus records. Only I, the Illusive Man, a small team of cloners at the Womb facility and the researchers we chose to monitor the clones, would have any knowledge of the project."

Dr. Martin became more animated as she continued, obviously enjoying talking about her work. "Clones would be grown in an accelerated process over the course of a standard galactic month and would be given a basic level of understanding and cognitive function through neural implants and subliminal training. Once capable of cognitive thought and action, they would be delivered here with a paired researcher for study and basic training."

"What about the children? Did some of your researchers succumb to my charms and fall for their research subjects?" Shepard asked drily, still trying to comprehend what the director was telling him.

"Eugenics experiments, Commander, nothing more. We were interested in seeing what else your genes could produce."

"How do you expect farmers and laborers to command ships and men in war, Doctor? These aren't the kinds of things that can be crash-taught in a classroom."

"A valid point, and one my colleagues brought up. Initially, the plan was to replicate your education and experiences, at an extremely accelerated rate of course. This failed when we realized our files regarding your life and interactions were too incomplete to adequately replicate your life experiences."

"It was the Illusive Man who brought us an answer. His research into the Protheans had uncovered a previously unheard of ability they apparently all shared: the ability to store and share memory and experience through touch. Similar to your report on your experience with the beacon on Eden Prime during the skirmish with Saren, a Prothean could touch an object, biological or synthetic, and instantly know its entire history and function."

"Somehow, the Illusive Man found a way to imitate this process and created a device that could scan an item, or in this case a person, then imprint that knowledge and detail on another. This is how we would create multiples of you, Commander."

Dr. Martin paused for a moment, letting Shepard grasp the implications of this technology before resuming her story.

"Of course, the first trials were failures. Apparently your body's last memories were of suffocating and disintegrating after the Collectors blew up your ship. Not the best memories to wake with, I will admit. Those clones suffered horribly, convinced they were still dying alone in space. We had to put them down."

"We eventually learned how to selectively edit your memories, to filter out the undesirable parts and leave only the parts that make you, Commander, an effective soldier. Our second stage of trials went better, but was still a failure. It turns out that, when confronted with multiple exact copies of themselves, the clone's first instinct was to eliminate the others. The bloodbath was quite shocking, really."

Shepard could only listen on in dull horror.

"Finally we settled on the current 'Crèche' plan. We found a remote, isolated planet capable of sustaining human life with only a basic level of technology and created this settlement. We created a template personality, altered individual details enough to prevent a repeat of the second test, and then used the modified template on the third set of test subjects. The subjects proved docile and willing to accept their lives as colonists and farmers, as you witnessed above. We maintain them in this 'Tabula Rasa' state to protect the integrity of our tests and allow the eventual personality wipe to happen smoothly."

"Wait" Shepard interrupted harshly, "what do you mean, personality wipe?"

"Once we receive the call from the Illusive Man to join the fight, we'll wipe the template personalities, load the modified combat personalities, and send them out to fight for humanity!"

"You're crazy, all of you!" Shepard shouted, struggling even more fiercely with his restraints. "It's bad enough you cloned my body. You're saying you cloned my mind as well? And, and, took an eraser to the parts you didn't like? WHAT GIVES YOU THE RIGHT!"

"Expedience, Commander. Just as expedience will ensure that you won't say anything to the subjects while you're here. We wouldn't want a repeat of the second trial now, would we?"

"What makes you think I'm going to quietly go along with your plans here, Doctor?"

"You won't have a choice, Commander. We've confiscated your weapons and armor, as well as your communicators, just as we did with your companion. Tomorrow you will wake up, go to the fields and work with the other subjects. We will keep Dr. Tsoni here, so that she can perform her duties like a good wife. You will have an opportunity to talk with her in the evening."

Dr. Martin returned to the computer terminal before looking up, as if she had forgotten something. "By the way, I wouldn't recommend trying to contact your ship. Just because we don't have any obvious defenses here doesn't mean we're entirely defenseless. Should your ship decide to break orbit or send another shuttle down, please know that you and your Asari friend will be dead before they touch down."

"And please don't try to run. We wouldn't want to have to send the clones after you."

Looking down at her console, Dr. Martin pressed a button before looking back up. "Now, I think it's time for you to sleep. You have a very busy day tomorrow, _Brother_ John."

Shepard felt the prick of a needle against his neck, before consciousness faded for the second time that night.


	3. Chapter 3: Pollux

Chapter 3 – "Pollux"

The idea for the memory transfer device came to me during a morning shower. As is my wont, I tend to do most of my thinking in the shower (not much else to do in there while soaking). I was pondering how to have clones of Shepard that were actually useful, rather then mindless physical copies of Shepard intended to eventually be indoctrinated and turned into shock troopers by Cerberus.

Eventually I remembered Javik, the Prothean companion that came with the "From the Ashes" DLC, and his reveal about how Protheans obtained information from things merely by touching them and concentrating. The memory transfer device was an extrapolation of that idea, twisted by TIM and Cerberus into a tool to further their goals. We know from novels and comics set prior to the games that TIM has/had an interest in the Protheans. It seemed reasonable that he had his own sources regarding their abilities and history, and would find a way to make use of the things he discovered. The 'failed trials' sequence was an outlining of some of the problems that might (in this story 'did') occur from putting such a device into actual use.

* * *

Sunlight shining through the window fell on a sleeping Shepard. Sounds and images crossed his mind; armies of soldiers in Cerberus armor fighting wars across the galaxy, rolling over armies of Turians and Krogans and Asari like an inexorable tide. And every soldier had Shepard's face.

With a gasp, Shepard woke, clutching at the sheets. Looking around, he found himself in a small room, lit by a single covered window. The bed beside him was empty. Recalling the events of the previous night, Shepard swung out of bed and searched the floor around the bed. A barely noticeable groove circled the bed. Before Shepard could probe further, though, a knock at the door presaged the entry of one of the colonists.

"Good morning, Brother John. That was quite the party last night, eh? Don't worry about the hangover, a bit of sweat and exertion will work that right out of you. C'mon, you'll want to get some breakfast before we head out to the fields."

Looking down, Shepard found himself already dressed in colonial work clothes like those the clones wore. Pulling on a pair of boots, Shepard stamped his feet, a bit surprised at how well the boots fit. _Then again, it's not like they don't know my foot size around here._

Leaving the building, Shepard found the rest of the clones gathered near the central platform, talking and eating. "My name's Alex, by the way", his guide said. "You've been assigned to my work crew." Alex shoved a protein bar and a cup of juice into Shepard's hands. "Here, eat up before we head out. I'll go get our supplies from the quartermaster." With that, Alex wandered off, leaving Shepard alone with his breakfast.

Several of the clones wandered by, patting Shepard on the back and welcoming him once more to the family. Some expressed commiseration at his work assignment. Apparently John and Alex had been assigned to the furthest field that day, the trek to which would take the better part of an hour and leave them isolated from the rest of the brothers.

Eventually Alex returned carrying two satchels filled with agricultural tools and a wide-brimmed hat. The hat turned out to be intended for Shepard. "Till you get used to it, you'll want to protect yourself from the sun out there. It's easy to overheat working in the fields and I'm not going to carry you all the way back here if you faint" Alex said, jokingly. At least, Shepard hoped it was a joke.

Shepard reached for one of the satchels, grunting with the weight as Alex released it to him. "Another thing you'll have to get used to, I'm afraid. The soil where we're headed is a bit tougher then the other fields, so our tools have to be denser to cope. Alright, let's head out. Sooner started, sooner finished, right?"

Shepard sighed. "Right."

After an eternity spent working in the broiling sun, Shepard's body screamed with exhaustion and wear. Leaning against his hoe, Shepard watched as Alex patiently turned the soil in a long furrow on the opposite side of the field. Reaching the end of the row, Alex looked up and spotted Shepard. "Time for a break" Alex called, setting down his hoe and walking over to where they had left their bags. Shepard longed to join him, but his body refused to listen. Instead, he sat down there in the field.

Soon, a shadow fell over him as Alex approached, carrying a water bottle and a soaked rag. The rag was put over Shepard's head, once his hat was removed, and immediately began cooling him as the water leaked over his face and down his neck.

"It's tough working out here, but this field produces the best melons you've ever tasted, trust me. It'll all be worth it come harvest time. My wife makes a scrumptious baked-melon bread, just you wait."

Alex sat down next to Shepard, taking a long swig from the water bottle before handing it to Shepard. Shepard fought the urge to pour the bottle down his throat, instead taking a long swig like Alex. The water was luke warm and tasted of leather, but in Shepard's dehydrated state it tasted like purest glacial spring water.

"So, picket fence or blue barn?" Alex asked while gazing at the field.

"I'm sorry?" Shepard asked, puzzled.

"Your dream last night; white picket fence or a blue barn? Everyone here dreams of one or the other. It's odd, really. None of us remember actually seeing either of those things. We had to ask the wives what they were. But, for some reason, everyone dreams of one or the other."

Remembering his dream of armies of Shepards conquering the galaxy, Shepard suppressed a shudder. "I don't remember my dreams, Alex, so I couldn't say."

"Maybe it's a family thing. Funny, though, if you think about it. Take our family, for instance. I'm sure you've noticed by now that we all look alike, right? Alex asked while tucking his medium length sun-bleached hair back behind his ears. "Our wives tell us that that's natural, since we're all related. But I happened to overhear a couple of the wives talking awhile back. Turns out they're sisters also, but they looked nothing alike."

Shepard remained silent, unsure what he should say and mindful of Dr. Martin's warning about revealing the truth to the clones.

"Something is off about this place, John. Watch what you say, especially around your wife." With that, Alex stood up and went back to work.

The day mercifully came to an end with the field plowed and ready for seeding. "Alright, good work today, John! I don't know about you, but I'm craving a big bowl of soup and a nice warm compress when we get home. Tomorrow we'll bring a couple of brothers with us and start seeding."

Shepard could only nod numbly, dreading the long hike back with the heavy tools on his back.

"So what kinds of meals does your wife make?" Alex asked cheerfully as they began walking back to the settlement. "Mine does a wonderful vegetable stew, full of big chunks of vegetables and a delightfully thin broth. She even does biscuits on special occasions, and they barely get burnt at all. I don't mind saying, our brothers talk all the time about how well-off I have it, having such a wonderful wife."

"Liara doesn't really cook." Shepard tiredly responded.

"Is that your wife's name? Liara, huh? Seems a bit of an odd bird, what with that weird cap and all. No offense meant, of course. It's just that she didn't seem to be getting along too well with the other wives. Ah, well. I'm sure she'll perk up once she gets to know them. It never seems to take the new wives long to get into the swing of things around here."

Shepard grunted in agreement. Alex eyed Shepard for awhile as they walked, as if assessing him somehow.

Finally, Alex's voice dropped into a low whisper as he pulled close to Shepard. "Thing is, none of us really know much about the women, even our own wives. How we met, what made us fall in love, or even why we decided to come here. One minute nothing, the next we're being introduced to our long, lost family, with loving wives on our arms. Oh sure, we all have memories of our parents and childhood, but nothing between then and coming here."

Shepard listened closely, no longer quite as tired. Could these clones have figured out the truth on their own? "Have you talked about this with anyone?" Shepard asked, dreading the answer.

"Out in the fields, we talk. No one there to listen in and lots of time to sit down and compare notes. That's where we figured out about the dreams, how we all had either the one with the picket fence or the blue barn. One of our brothers decided to talk to the women about it, so he went to his wife. Only thing is, that night he got real sick and had to be taken to the med center. And the next morning we had a body to bury. We'll pass by the graveyard on the way back to town and you'll be able to see the grave."

"What about the wife of the dead man, the one he talked to? What happened to her?"

Alex shrugged. "Don't know. We never saw her after that and the wives refuse to talk about either of them. It's like they never existed." Alex studied Shepard more closely. "And your lack of a reaction tells me you know something about this. Don't you?"

Shepard struggled with a response while Alex waited, studying him. Finally, Shepard gave up. "I'll tell you what I know, what I've figured out, but only out in the field. Tomorrow. You said we'd need some more brothers to help plant the seeds? See if you can get some of the brothers you've talked to before about all this; try to get them assigned to our field. The ones who have questions like you."

"Alright" replied Alex after a moment, "I'll see what I can do. I can think of a couple of people who'll want to hear this. But first, tell me this one thing. Are you really our brother?"

Shepard sighed. "In a very general sense, yes, I suppose you could say I'm related to all of you. We'll talk about the specifics tomorrow."

That night, Shepard finally had a chance to talk with Liara again. Like the other wives, she met him at the edge of the settlement to welcome him home. Taking her in his arms like the other men, Shepard whispered in her ear. "We have to talk. Not here. Somewhere loud, somewhere we won't be overheard." Liara nodded, inclining her head towards the kitchen area where a large number of couples had gathered.

Putting his hand around her waist, Shepard walked with Liara over to the kettles where Liara ladled out a bowl for Shepard and herself. Sitting down next to a particularly loud generator, Shepard took a spoonful of the vegetable stew. It was incredibly bland, with very few spices and severely overcooked vegetables. Liara leaned against his shoulder, holding her bowl, and began talking in a low voice.

"They told you what's going on here last night, didn't they?"

Shepard nodded, eating another spoonful from the bowl.

"I'm so sorry." Shepard looked into Liara's eyes. "James was right; we should have 'glassed' this place from orbit rather then come down here."

Shepard shook his head "No, we needed to learn about this place. If the Illusive Man went this far with his plans, who knows what else he has out there. Maybe a fleet of Normandys flown by clones of Joker, just waiting for my clones to command them?"

"In that case, what are we going to do about it?" Liara asked, looking back down at her untouched bowl. "You're out in the fields all day, while I'm constantly being watched by the researchers. Even now they're monitoring us, waiting to see what you're going to do."

"I've got a plan. Some of the clones have started to figure things out for themselves. If I can get them to understand the whole truth, and organize them against Cerberus, maybe we can disable Martin and her crew before they decide to kill us."

Shepard took another spoonful of the stew, willing himself to appear casual as he continued. "They disabled my comlink with the Normandy, and they said they did the same to yours. But EDI and Garrus should still be keeping an eye on us from orbit. While I'm talking to the clones, I want you to find a way to signal them, make sure they're ready to assist should things go pear-shaped down here. Blinking lights, smoke signals, I don't care how. Just find a way to warn them."

Liara finally ate a bit of her stew, grimacing at the taste. "I think I know a way. When we were first caught, I convinced them I was assigned to your crew by the Illusive Man himself, as part of your support staff. They seemed to buy it since they think you're still working for him."

Liara continued after another spoonful of soup. "I'm being watched, but I should be able to get access to the communications room below for a moment. That would be all I'd need to contact the Normandy."

"Just be careful, Liara. The clones have been telling me about others who asked too many questions. They're not squeamish about cleaning up loose ends around here."

"Leave it to me, 'husband', this is woman's work after all" Liara said with a smile.

The next day, Shepard and Alex left for the field with three other brothers, each of them carrying a large sack of seeds for planting. After working for several hours, the men took a break, taking shelter from the blazing sun under a large tree. Each of the men looked towards Shepard expectantly.

"Alright, first I should probably introduce myself properly." Shepard took a deep breath before continuing. "My name is John Shepard and I'm the Commander of the SSV-Normandy, an Alliance space vessel."

"A lot of what I'm going to say isn't going to mean much to you. A lot of information has been kept from you, things about who you are and what your role is in the larger galaxy. I'll answer what questions I can, but first I need to explain why I came here."

The men looked at each other but otherwise remained silent, waiting for Shepard to continue.

"Nearly four years ago, my ship was attacked by a group of beings called the Collectors. They destroyed my ship, killed most of my crew, and nearly killed me. An organization called Cerberus found my body and spent the next two years trying to bring me back to life. Eventually they succeeded. For their own reasons, they provided me with a new ship and a crew to hunt down the Collectors and make them pay."

"During that time, I learned a lot of things about Cerberus, things I don't agree with. Once the Collectors were dealt with, and due to those reasons, I severed ties with Cerberus and rejoined the Alliance."

"A week ago a threat from outside our galaxy, called the Reapers, attacked Earth, my home and home to many more like me. I barely managed to escape with my ship and crew and set out to find allies to help drive off the Reapers and take Earth back. That's what brought me here."

Shepard paused for a moment to think before continuing. "Here's where all of you come in. While I was being revived by Cerberus, the scientists healing me tried many things, like cybernetic enhancements and tissue augmentation. One of those things, I've recently learned, was cloning. Cerberus took my genetic information, the basics of what makes me who and what I am, and created identical copies of me."

Shepard looked into Alex's eyes. "When you asked me yesterday whether I was your brother, I told you that, in a general sense, I was. That was a lie. You are not my brothers, you are _me_. You are clones of me, made by Cerberus just in case I died before doing what they wanted me to do. You were given memories, temporary memories, and artificial lives until Cerberus could come for you and turn you into weapons."

Shepard expected denials, angry denouncements, even claims of insanity. Instead the men looked troubled, and thoughtful. Alex merely nodded, as if it all made sense. After a while, Alex asked "So then, our wives? Who are they?"

"Cerberus scientists," Shepard responded, "responsible for monitoring you and keeping you safe and ignorant until Cerberus comes for you. That's why you don't have any memories of meeting them. Until you arrived on this planet with them, you had never met."

"What about the children?" one of the other men, Shepard thought his name was Marcus, asked.

"More experiments. They wanted to know what would happen if you or I were to conceive a child."

"That explains why I'm never allowed to play with Sarah, I guess. Damn witch! First she steals my life then she steals my daughter." Marcus muttered angrily.

Each of the men agreed with Marcus, patting him on the shoulder. Alex turned back to Shepard. "So, what are we going to do about this? If what you say is true, they're not going to just let us go if we ask nicely."

"There's a command center buried under the settlement, a sort of common building where they can meet in secret and review their notes. My first night here, I was drugged and brought down there so they could question me."

"Tonight, when we go back, I'm going to find a way down there on my own. While I'm doing that, I want each of you to talk to your brothers and tell them what I've told you. When we act, it's going to have to be fast. The woman I came with, Liara, is my friend, not a Cerberus agent. She's finding a way to contact my ship now. They'll support us once we begin, but the initial conflict is ours to deal with."

Shepard propped himself up on one knee and began sketching in the dirt. "Here's my plan…"


	4. Chapter 4: Cain

Chapter 4 – "Cain"

Originally, the planet Shepard found while scanning was going to be an idyllic farm planet, full of simple people who were strangely unaware of events outside their small community but who were otherwise non-descript. Over the course of several 'away missions' (think Star Trek), Shepard and his crew would uncover oddities and discrepancies before finally uncovering the truth about the clones. Initially they would make the wrong assumption, believing the clones were the Cerberus agents responsible and the women were innocent. Shepard would then be disabused of this notion with the reveal that the women were not only aware of the situation, but were behind the whole thing. I even toyed with the idea of an apparently misogynistic society on the surface (men treating the women like medieval property), which would cover the truth of an unseen societal arrangement which was almost completely the opposite.

This idea fell apart due to in-story time constraints. Shepard and the Normandy simply don't have the free time to spend days or weeks casually dallying on a remote planet while the Reapers are busy doing their thing to Earth and the rest of the galaxy. This revelation wound up affecting large parts of the plot, leading to the somewhat rushed feel of events in the story.

This is the penultimate chapter of "Project Gemini". Enjoy.

* * *

The sun had already set by the time Shepard's work group returned from the fields. As before, the wives awaited them at the edge of the settlement. Shepard had instructed each of the men to act as they normally would; stressing that, until they made their move, the wives would have to suspect nothing.

Shepard searched for Liara, finally noticing her near the kitchen fires. Just like the previous night, Shepard took the proffered bowl of soup and led Liara over to their spot by the noisy generator. While scooping out a spoonful of soup, Shepard felt an odd shape in the bowl.

"A master keycard," Liara explained around a mouthful of soup. "I swiped the blank from the research lab and recoded it to work on all the doors."

"What about the Normandy?" Shepard asked, raising his spoon as if to blow on the hot soup. "Were you able to let them know what's going on?"

"Not yet. Most of the women were there working on something. I think they were trying to get in touch with the Illusive Man." Liara responded.

"Then time is running out. The men I worked with are talking with the others tonight. Things are going to come to a head soon. I need to find the armory, or whatever they're using for weapons, and make sure they can't use them against us."

"You'll need that key then. Their system security is light so I should be able to hack in and monitor things from one of the offices without being noticed. But you'll have to move fast."

Shepard put the bowl down, surreptitiously palming the small ID card from the bowl. "We move tonight. Those weapons need to be secured before things up here come to a boil. Once we have the weapons and the women are restrained, we'll call the Normandy down, get everyone on board, and get out of here before Cerberus arrives."

"Don't forget the data, Shepard. I don't think you want Cerberus starting this experiment all over again as soon as we go."

"You're right. Once we've got the women restrained, do what you can to purge the data while we're loading. Anything else?"

"Just be careful, Shepard. The Illusive Man was right about one thing: we can't afford to lose you, especially not now."

* * *

That night Shepard searched around the bed, hoping to find a trigger or switch to activate the lift down to the underground lab. On her previous visits to the command bunker Liara had used the main entrance located in the medical clinic. However, she agreed that there were probably lifts in each of the residences to make it easier to bring unconscious clones in for emergency treatments and procedures.

According to the men Shepard had talked to, each of their wives slept on the right side of the bed every night, so Shepard began by examining that side of the bed while Liara kept watch. Sure enough, a small cover on the head board just behind the pillow lifted to reveal a small switch. Getting back on the bed and motioning to Liara to join him, Shepard flipped the switch, causing the bed to slowly lower into the floor.

Shepard tensed as the lift came to a stop in a darkened lab. Quietly getting off the bed, Shepard snuck to the door as Liara began activating the nearby computer. Seeing no one in the hallway outside, Shepard returned as Liara finished hacking into the computer system. Bringing up a floor plan of the complex, Liara pointed to a small room at one end of the facility. "Armory", she said in a quiet voice before pointing to another room, this one more towards the center of the facility "Communications". Finally she moved her finger to a point about midway between the two.

"This is us. This room is as good as any, so I'll stay here and try to keep you off their sensors." Reaching into her pocket, she produced a small earbud communicator and a vocalizer patch, which she handed to Shepard. As Shepard put the earbud in place a message crossed the screen before them.

"It looks like something is going on up above." Liara said, switching to a live feed of the surface. An image of the central platform appeared, showing several men gathering in the orange artificial light along with a group of the women who looked increasingly alarmed. Shepard recognized Alex and Marcus among the growing crowd.

"It's starting. I'd better get that armory secured before things turn violent." Shepard said, turning away from the computer and towards the door. "Keep me informed if anything changes."

"Yes, Commander."

* * *

Shortly after leaving the room, Shepard heard Liara's voice in his ear.

"Shepard, it looks like Dr. Martin was able to make contact with the Illusive Man. He's sending troops to collect the clones."

"Understood. What about the surface, what's going on?"

"The clones are saying something. It looks like they're angry. One of them is pointing at the women. Wait, a group of the women are confronting the men. Tempers are starting to fray out there, Shepard."

"I'm almost at the Armory now. Do you see any weapons? Are any of the women armed?"

"No, not that I can see. Right now they're acting confidant but they're definitely afraid. They're probably waiting for their commander to do something."

"I'm at the Armory." Shepard said then paused, hearing footsteps coming down the hallway. "Sounds like I have company. One sec." Shepard ducked behind a bulkhead as a group of women ran down the hallway towards the armory. As they passed, Shepard jumped them from behind, tackling the women and driving them to the floor. Elbows and knees cracked on the hard floor as he landed on the women, stunning them long enough for him to quickly grab their heads and slam them into each other, knocking them unconscious. Remaining crouched over the bodies, Shepard listened intently for sounds of more company.

Hearing nothing further, Shepard pulled the unconscious bodies towards the armory door then used his keycard to open the door and deposit them inside. Searching the shelves and racks Shepard quickly found his armor and weapons which he immediately began donning. Suddenly the door opened to admit a disheveled Dr. Martin, apparently just awoken from her sleep by the disturbance on the surface.

"I don't care how panicked you fools are, I'm not going to let you destroy all of our hard work just because the subjects caught wind of the experiment." she began in a sharp voice, obviously continuing a previous argument and oblivious to Shepard's presence. "Listen, all we have to do is use the knockout gas to put them to sleep. Then we'll be able to take our time getting them all re-prog…" Dr. Martin trailed off when she finally noticed Shepard in the room and the pistol aimed at her head.

"You'll be able to do what, Doctor? Wipe their memories? Reprogram them into mindless cattle?"

"Shepard! What are you doing here?"

"The experiment is over, doctor. No more clones, no more memory wiping, no more playing God. It's all over." Shepard flicked the pistol briefly away from Dr. Martin, indicating she should move away from the door.

"So you're behind this? I should have guessed, as soon as I saw you with that mongrel alien filth. The Illusive Man told us you were a rogue agent. He wants you apprehended you as quickly as possible." Dr Martin slid towards one of the equipment racks, eyes flickering over the shelves, looking for a weapon.

"Not going to happen, doctor." Shepard suddenly lashed out, his fist hitting Dr. Martin in the face. She immediately crumpled to the ground, unconscious and leaning against the equipment rack. "And that's for that 'mongrel alien' crack."

Resuming his search of the armory, Shepard found a small closet filled with ammo crates. Removing the crates, Shepard stuffed the bodies of the two researchers into the closet then locked the door using the nearby panel. Returning to his gear, Shepard finished reloading his pistol, which had been used quite effectively to threaten Dr. Martin even in its unloaded state.

"Liara, I've got the doctor knocked out. Two of the researchers are locked up in a storage closet over here. What's the status on the surface?"

"Not good, Shepard. A full-on fight has broken out. We've got scuffles between the clones and the researchers all over the place. No weapons so far, but it's only a matter of time till someone remembers those farming tools. A couple of the clones pulled the children aside and are sheltering them in one of the buildings."

"Dr. Martin mentioned using knock-out gas. Can you disable the emitters from where you're at?"

"Let me check." Liara went silent for several long seconds before returning. "No, they've locked me out of those controls. It looks like they found my hack and they're disabling it."

"Alright, I'm on my way to you with the doctor, maybe we can use her to regain access. We'll head to the command center and take control there."

"Acknowledged, Shepard."

* * *

Shepard returned to the lab dragging the unconscious Dr. Martin and waited on guard while Liara donned her armor and weapons, reclaimed from the armory by Shepard. Re-equipped, the pair made their way through the hallways, Liara guiding them using a map she loaded onto their Omni-tools. At one intersection they ran into a group of researchers armed with riot sticks, probably sent to locate Dr. Martin and subdue Liara. Liara made short work of them, lifting them into the air with her biotics and slamming them repeatedly into walls, ceilings and floors. Finally she let them go, dumping their battered bodies to the floor.

Shepard took aim at several points, but hesitated. For some reason he was unwilling to pull the trigger on the researchers, who he felt were still non-combatants despite their arming themselves with basic weapons. He wanted to scold Liara for the savageness of her attack, but decided she was probably just releasing her stress from the last couple days. Instead, Shepard checked them for consciousness and vital signs before continuing towards the command center.

They arrived at the command center to find a group of four researchers clustered around the main monitor, watching events unfolding on the surface. "Get your hands up and back away from the terminal." Shepard declared, stepping into the room with his pistol raised and threatening. "Now!"

Liara, floating Dr. Martin in the air with her biotics, followed him into the room as the women gasped and spun towards Shepard. Slowly they raised their hands and followed Shepard's directions to a corner of the dark room, where Liara tied them up along with Dr. Martin, who was starting to regain consciousness.

Once the researchers were secured, Shepard returned to the primary monitor, a large screen filling almost the entirety of the wall upon which camera feeds covering most of the surface and the underground facility displayed their images. It appeared that the fight on the surface was coming to the end. Most of the women had surrendered and were sitting clustered on the central platform under guard by a large number of clones. A few researchers still fought, but were slowly being overwhelmed by the stronger, tougher clones.

Beside Shepard, Liara work hurriedly at the terminal. Finally she looked up at Shepard. "I've got the gas emitters disabled but long range sensors are showing a Cerberus frigate in orbit. Shepard, it's launching shuttles."

"How long until till they get here? Do we have time to evacuate the clones?"

"Shepard, they're already…" A sudden roar of engines presaged the landing of two Cerberus shuttles in the middle of the settlement. "…here," Liara finished.

"Alright, contact the Normandy, have Joker take out that frigate before it can send down any more troops, then send Jake and Garrus down with the shuttle. I'm going to head to the surface and do what I can till they get here."

"It's too late, Shepard" Dr Martin called from the corner. "Those troops will back up my team and put down this little rebellion of yours. Surrender now and maybe we'll find a place among your brothers for you."

Shepard opened his mouth to argue with the doctor, but was interrupted by a sound from Liara. On the screen, the Cerberus troops had cordoned off the area and separated the clones from the researchers. "Shepard, go! Before it's too late."

Shepard ran from the room, guided by Liara's map towards the main elevator out of the underground facility. While waiting for the elevator, Liara kept him apprised of events on the surface.

"Shepard, they've got the clones mostly subdued. Some are putting up a fight but they're being beaten down quickly. The researchers aren't fighting, but they aren't being treated any better. Hold on, they're bringing the children out of the building. Wait, what are they…? By the Goddess, Shepard, hurry! They're shooting the children!"


	5. Chapter 5: Able

And so, here we are at the finale. This chapter throws in some alternate points-of-view for emotional effect (and other reasons, and you'll find out once you read it evil grin). This chapter was a lot of fun to write, being my first 'final' chapter. The idea for the ending came to me as one of two possible outcomes. The other may get used in the sequel I'm contemplating. If I decide to write it (I have the plot seed, still need to decide how and where I want it to end up) I'll post details here, so keep an eye on this space.

Thank you for sticking around and, more importantly, reading this work. It's been a long, strange trip since that case of 'misapplied trope' back in March that starting this whole mess. Now, I'll leave you to the finale. Enjoy. - Lapis Dragon

* * *

It had been a strange day for Marcus.

First, Janet had let him kiss his daughter at breakfast before leaving for the fields with Alex and John. Marcus treasured every moment he was allowed to spend with little Sarah, which were few and far between thanks to Janet's constant interference.

The second strange thing occurred out in the fields, when John started talking about spaceships and aliens and great fights out among the stars. Marcus hadn't had a chance to get to know John well yet, but something about the way his brother spoke made Marcus want to listen and believe. Marcus could tell by Alex's face that he believed as well.

Some of the things John spoke of confused Marcus, and some angered him, especially when he began talking about the women. According to John, the reason Janet wouldn't let him spend time with Sarah wasn't because he had 'been bad', as she often claimed. The reason he wasn't allowed to be with Sarah was because Janet and the other women wanted Sarah all for themselves. This, more then anything else John said, made him want to take part in John's plan to punish the women.

Marcus tried to listen as John explained his plan, but Marcus' thoughts were focused mainly on his own plan to get his daughter back. When they got back that night, Marcus would confront Janet and tell her that he wanted to have a greater role in Sarah's life and if Janet tried to fight him, well, Marcus would show her just how _bad_ he could be!

* * *

That night, after returning from the fields and having dinner with Janet and Sarah, Marcus struggled with himself; keeping his anger restrained so as to not frighten Sarah. Finally, Janet put Sarah to bed and joined him in the main bedroom. But before Marcus could start his argument, a commotion outside drew his attention to the bedroom window.

Outside, some of Marcus' brothers had gathered and were talking with loud, angry voices. Janet tried to order him to remain in the bedroom, but Marcus was fed up with dealing with her so he ignored her and went outside to join his brothers. Alex was already out there by the time Marcus arrived. From the looks of things, most of the community was awake by now, with the brothers clumping up in the center and the wives forming small groups around the edges. Marcus could feel the tension in the air.

"That can't be right, Alex" argued James. "Michelle wouldn't lie to me like that." Several of the brothers called out agreement with James, though just as many shook their heads in disagreement.

"That's the thing, James" replied Alex, patiently. "We've all been lied to our entire lives. We've been nothing but lab rats to them. Or do you really think Michael died of 'food poisoning' after arguing with his wife that night?"

"I don't know, Alex. It all seems awfully far-fetched."

Suddenly one of the elder wives stepped forward, flanked by two of the women. Mary was Alex's wife and had been married to him as far back as Marcus could remember. Marcus had always thought of the brown-haired, heavy-set woman as being soft spoken and kindhearted, at least compared to Janet, but tonight he could see thunderclouds forming in her eyes.

"What is going _on_ here, Alex? All of you need to go back to bed, this moment! Honestly! Why are you disturbing everyone's sleep at this hour of the night? You know full well you've got a busy day in the fields tomorrow. And yet here you are, making a ruckus with your friends, keeping all of us awake with your yammering!" Mary went on for sometime, haranguing Alex and the other brothers for what seemed like forever to Marcus. Finally Mary paused to take a breath. "Well? What do you have to say for yourself? Nothing, I'm sure. Now come to bed, this minute!"

Alex was silent for some time, head lowered as if he was ashamed with himself. Finally, in a voice so quiet Marcus almost missed it, Alex spoke one word.

"No"

This seemed to take Mary aback. "What did you say? Stop mumbling Alex, you know how I hate it when you mumble!"

"I said 'No', Mary" Alex repeated, this time raising his head and speaking with angry authority. "No more orders. No more commands, no more quiet threats. No more!

Mary's jaw hung low, her mouth working silently.

"I know about Cerberus, Mary. I know what you intend to do to us. How long did you think you could keep it a secret? All of us know now, Mary. Every single one of us." Alex took a threatening step towards the three women, who cowered before his looming anger. "We know, and we are not amused."

Mary, her face purpling in anger, straightened herself and slapped Alex across the face. Alex didn't even flinch. Instead, as if something primal had suddenly snapped loose inside him, Alex lashed out with his fist and buried it in Mary's gut, sending her to her knees with a choking gasp. And that's how the third strange thing, the fight, began.

* * *

The fight was mostly over now. Marcus made sure to protect Sarah and the other children while the adults fought. Marcus would have a hard time explaining things to Sarah, but at least now he would have the opportunity to do so, with Janet being one of the women under guard in the center of the community.

A sudden roar shook the community as two box-like… things… came out of the sky, noise and light flaring from the ends of odd legs as they landed on their bellies in the midst of the fighting. Out of the boxes poured men in heavy white clothes with black masks covering their heads and faces entirely. They pointed odd sticks at the men and shouted orders which Marcus couldn't understand over the roar still coming from the legs.

Some of the men ran towards Marcus. He tried to fight them off and protect the children but they quickly forced him to the ground and held him there. These men were stronger then the women; much stronger then even Marcus. One of the men went into the building and began dragging the children outside.

The women looked relieved to see the strange men and began getting to their feet. Janet shot Marcus a terrifying smile, full of anger and vengeance. However, the strange men quickly forced the women back down to the ground, wiping the smile off Janet's face and replacing it with a look of fear and confusion. This worried Marcus even more then her smile had.

Marcus returned his attention to the children. They had been lined up against the building and one of the men was pointing his stick at them. Something about the way the man stood worried Marcus greatly. Suddenly a pop sounded from the man's stick and one of the children collapsed to the ground. Marcus couldn't understand. The man had done nothing other then point his stick, but there was Jake's son lying in the grass, not moving. Another pop sounded and Simon's daughter fell to the grass as well. The next child in line was Susan.

Strength flooded through Marcus' limbs as he threw off the man holding him down. He roared, running towards the children. Before he could get there, other men tackled him as another pop sounded and Susan crumpled to the ground. Marcus broke free from the men trying to restrain him and ran towards Susan. She wasn't moving and a small red stain was blooming on her tiny chest. Marcus shook her, called out to her, anything to get her to respond.

Nothing.

A red film of rage descended on Marcus. Screaming in grief, Marcus turned on the man with the stick, leaving Susan in the grass as an unquenchable desire for blood and pain filled him. Marcus barely felt the sting as wounds opened in his chest and arms. He descended on the man with the stick, grabbing him by the neck with both hands and wringing him like an old shirt. Other men pointed their sticks at Marcus, who turned on them and pounded them into the ground, grabbing them by their arms and legs and swinging them into each other. Finally, his strength fading and the pain of his wounds becoming unbearable, Marcus returned to tiny Susan, once more taking her into his big, blood-stained arms and holding her before everything faded to black.

* * *

Shepard arrived on the surface just in time to watch in awe as Marcus rampaged through the Cerberus forces. The man must have had Krogan blood flowing through his veins. What's more, his rampage seemed to snap the other clones out of their stunned stupor. All around the settlement clones fought with Cerberus troops. Unfortunately, despite the renewed vigor Marcus' fight had instilled in them, they were still no match for the armed and armored Cerberus forces.

Shepard took advantage of the confusion to flit from cover to cover, taking out Cerberus targets as he went. It wasn't enough. A grenade went off near the central platform, killing most of the women and scattering the rest. Elsewhere a Cerberus trooper fired wildly, killing several clones before Shepard took him out with a single shot to the head. Most tragically, a pair of troopers caught the children, huddling together in fear, in a cross fire and killed them.

By now the survivors had started to work together, guided by Alex and protected by Shepard. The Cerberus troops retreated to one of the habitat modules and began to take shots at the survivors still out in the open. Shepard joined Alex in cover.

"What happened, John? I thought we were just going to deal with the women?" Alex angrily demanded, pulling the bleeding body of one of the women into cover with him."

"It's Cerberus, Alex. Dr. Martin managed to contact them before we could neutralize her. They've come to collect you, or at least to mop up the experiment. I don't think they expected you to fight back like this." Shepard raised his head above the cover, firing a quick shot at the troopers before ducking back down as their return fire hit the wall behind him.

"What do we do now? They're just going to kill all of us out here."

"There are weapons in the bunker below. Signal the others and run to the medical clinic. There's a platform there that will lower you down to the bunker. Liara will show you how to use the weapons while I cover for you up here."

"But what about you?"

"I'll join you as soon as you're all safe. Trust me. Now go!"

Shepard rolled out of cover, spraying rifle fire across the building where the Cerberus forces were hiding. Shots pinged off the crates and walls around him as Alex and the survivors ran for the medical clinic. Shepard gave them a few moments of cover fire before returning to cover himself. Looking around, Shepard was dismayed to see even more bodies lying on the ground. Very few had made it to the building. Fortunately, Alex appeared to have made it.

Rolling from cover once again, Shepard threw a grenade at the building and ran for the medical clinic and the elevator. A bullet went through his thigh and another through his shoulder, causing him to stumble and fall behind some crates. Leveraging himself up, Shepard expended his thermal clip on the Cerberus troops, killing a couple more. _There should only be a few left, but even one is a danger. Come on, Garrus!_

Stumbling to his feet once more, Shepard made it inside the clinic and rode the elevator down to the bunker. Shepard quickly disabled the elevator controls. Hopefully that would slow the Cerberus troops down somewhat.

In the command center Liara was tending to the survivors' wounds. Shepard was aghast at how few had made it. Other then Dr. Martin and the two researchers who had been manning the station, the only other survivors of the colony were Alex and another of the clones. One of the women had made it to the bunker, but Liara was in the process of closing her blankly staring eyes as Shepard stumbled into the room.

Liara stood up and ran over to support Shepard as he collapsed into a chair. "Shepard, Joker says they've destroyed the Cerberus frigate, but the shuttle bay doors were damaged in the attack. They're on their way, but they won't be able to land in the colony."

"There's only a couple of them left. If we can hold them off long enough, Garrus will be able to take them out by himself. Liara, show Alex how to barricade this room. I'm going to head to the armory and secure some more..." Shepard stopped as he noticed the two researchers he had left secured in the armory standing in the doorway holding grenades.

"No!" Dr. Martin cried as the two women armed and threw the grenades into the room.

* * *

To Liara, it was as if everything happened all at once. She noticed the two researchers at the same time Shepard did and instinctively used her mind to seize them, but not before Dr. Martin shouted and the two women threw their explosive devices into the room. Liara tried to divide her attention, just managing to catch one of the grenades and throw it back at the women, but she missed the second. At the same time the clones threw themselves over the doctor while Shepard tackled her, landing on top of her and shielding her as the grenades detonated. The shock wave was stunning, rendering Liara senseless for several moments. When she regained her senses, she found Shepard laying on top of her, unconscious. Rolling him off gently, Liara bit back a gasp. Both of Shepard's legs had been amputated by the blast, the limbs ending in bloody stumps just above the knee. His back was shredded and a slow dribble of blood leaked from the corner of his nose and mouth. Sitting up, Liara found almost everyone in the room in a similar state. Only Dr. Martin and the clone named Alex had appeared to escape the blast without significant injury. The other clone was dead, most of his head destroyed by the blast. The other researchers were in similar states, either dead or beyond saving.

All of this was secondary, though. _Blessed Goddess, don't let him die!_ Tearing strips from the lab coat of the dead researcher beside her, Liara tied tourniquets around Shepard's stumps, hoping to stem the blood loss. Leaning down, Liara determined that Shepard was still breathing, but barely, and each breath sounded more labored then the last. Seeing Alex help Dr. Martin to her feet, Liara called out to them. "Help me! Shepard is bleeding badly and I can't stop the blood! We have to get him to the med bay. NOW!" The two rushed over to Liara and Shepard.

Dr. Martin gazed down at Shepard, frowning. "Our med bay isn't equipped to handle something like that. I'm afraid we're going to lose him, unless we get him to your ship now."

"Isn't there something you can do? Anything!" Liara demanded, growing hysterical at the thought of losing Shepard in this way. Dr. Martin just shook her head in denial.

"There is one way, Doctor" Alex said in a soft voice, so quiet Liara almost missed it. "It may be the only way, if we still have time."

"Alex, you can't mean _that_? It might save him, but what about you?" Dr. Martin asked incredulously. Liara felt a pang of hope as a look of certainty filled Alex's face.

"It's the only way, Doctor. John told us what you said about him, about the reason why you decided to make copies of him. He's the most important person in the galaxy right now. I'm nothing but a simple farmer, but him? He's going to save us all."

"Alex, what are you talking about? Can you save him?" Liara asked, confused.

"Memory Transfer. We copy his mind and put it in another body. In this case, in Alex's" Dr. Martin replied. "But Alex, we would have to wipe your mind first. You'll cease to exist."

"It's what you wanted to do anyway, Doctor. At least this way, it's my choice." Alex bent to lift Shepard and gingerly held him in his arms. "Now quickly, before we lose even this slim chance."

"This way, the machine is in the lab over here" Dr. Martin called, running for the door followed by Alex and Liara. Rounding a corner, Dr. Martin fell back with a grunt, blood flowing from a gun shot to her gut. Liara grabbed the two Cerberus troopers standing in the hallway with her biotic field and ruthlessly crushed the life out of them. Helping Dr. Martin up, Liara led the way to the lab where Alex laid Shepard out on the table before climbing up on an adjoining one.

Dr. Martin, panting in pain, pointed to a console set into the wall and a cabinet holding two devices like thick headbands covered in electronics with wires streaming from the top edge. Liara set Dr. Martin in the chair at the console and ran to put the headbands on Shepard and Alex. "Thank you Alex." Liara said as she slipped the headband around his head. "Thank you so much. I'll never forget this."

"John is a lucky guy, having someone like you to take care of him." Alex replied with a smile. "I wish Mary had been more like you, even with your weird hair." Liara smiled back before returning to the console where Dr. Martin labored through her pain and blood loss to activate the machine. A hum built as the machine came to life, lights activating as Dr. Martin worked feverishly at the controls.

"I'm going to wipe Alex's mind first, so we have a clean base to overlay Shepard's mind onto. Keep an eye on Shepard, make sure he's alive until the transfer is complete. This won't work on a dead body. Once Alex is gone, I'll begin the transfer. When we hit 99% complete, remove the headbands. We don't want Shepard to remember the last couple minutes or we'll just have a repeat of the first trials."

Turning to look at Alex, Dr. Martin solemnly asked "Are you sure, Alex? This is your last chance to say 'no'." Alex merely nodded his head and closed his eyes, at peace with his decision. Dr. Martin flipped a switch and Alex flinched as green lights appeared on the headband. Liara chewed her lip as Alex's body twitched under the electric current, finally stopping when the lights on the headband went red.

"Now for the transfer." Dr. Martin said dully, her eyes glazing over as she fumbled with the controls. Liara hastily helped her trigger the command sequence. This time both bodies twitched as the lights on the headbands went green. Dr. Martin slumped over the console, her last bit of willpower depleted as she succumbed to her wounds.

Liara, remembering Dr. Martin's instructions, watched the console until it was nearly complete, then ran over to the bed and removed the headbands just before they went red. Both bands sparked in her hands, causing her to drop them. They shattered on the cold steel floor. On the beds, Shepard's ruined body stopped twitching, coming to a perfect stop. Leaning over his mouth, Liara felt his last breath leave as his body died. Shedding a tear over the dead body, Liara turned to the other table and Alex's body.

On the table Shepard's new body breathed slowly as his eyes fluttered behind closed lids. Finally, slowly, Shepard opened his eyes.

* * *

"Liara, what…" Shepard asked, slowly crawling back to consciousness to find Liara smiling down at him, tears in her eyes.

Shepard pulled himself up on onto his elbows, looking around the room. Dr. Martin sat in a chair, slumped over a console with a pool of blood underneath her. And on a table beside him lay a ruined body with his face.

"Alex, what happened? I…" Shepard paused, realization dawning as he looked down at his armor, finding homespun clothes instead of hardened ceramics. "Oh."

"He sacrificed himself for you. It was the only way." Liara said, tears pouring down her face as she helped Shepard to his feet. Together they left the room and returned to the surface to meet with Garrus and Jake. Neither Liara nor Shepard spoke of what had occurred below.

* * *

**EPILOGUE**

Shepard tossed about in his bed, finding sleep elusive.

After rejoining the Normandy, Shepard had instructed Garrus to fire on the colony with the Thannix cannon. All of the buildings, both above and below ground, were reduced to a rapidly cooling pool of superheated rock before the Normandy left orbit and returned to the war with the Reapers.

Despite the curiosity of the rest of the crew, neither Shepard nor Liara spoke of what had occurred on, and below, the surface of the planet. All they would say was that the threat had been dealt with. Still, Liara remained hesitant to speak with Shepard, even though both acknowledged that Shepard was fundamentally the same, in both body and mind.

Still, a war was being fought for Earth and the rest of the galaxy, and this new awkwardness would have to be set aside to be dealt with later. Somehow.

Shepard finally drifted off to sleep. In his dreams he was on Mindoir, back before the pirates had come to destroy it. Shepard, still a child, lay on the floor of his parent's habitat reading an old-earth storybook. It was a child's picture book about some farmer named McDonald and his many animals. Young Shepard flipped the page, gazing in childish delight at the farmer and all his various animals, posing in front of the farmer's house with its white picket fence and big blue barn.


End file.
